Dalglish was replaced by another playing legend when Graeme Souness took the reins after Dalglish's departure. Souness had enjoyed considerable success managing Rangers in the Scottish Premier League. He not only enjoyed success at Rangers but also courted his fair share of controversy, especially when he signed former Celtic player, and Catholic, Maurice Johnston from under the noses of their arch rivals Celtic. Under his leadership Liverpool won the 1992 FA Cup Final but his time as manager was overshadowed by an interview he did for the reviled Sun newspaper. Being interviewed was bad enough but for the interview to be published on the anniversary of the Hillsborough disaster meant that there was no way forward for Souness.

Souness himself was replaced by Roy Evans, another of Shankly's "Boot Room" assistants and Liverpool went on to win the 1995 Football League Cup Final. The writing was on the wall for Evans when Gérard Houllier was appointed co-manager in the 1998–99 season. The joint manager never was going to work and it came as no big surprise when Houllier became the sole manager in November 1998 after Evans resigned.

In 2001, Houllier's second full season in charge, Liverpool won an incredible Cup "Treble", when they won the FA Cup, the League Cup and the UEFA Cup. Houllier underwent major heart surgery during the 2001–02 season after he was taken ill during a league game against Leeds United. He returned several months later to a rapturous reception when Liverpool took on Roma, who were managed by Fabio Capello at the time, at Anfield in the UEFA Cup in March 2002. Liverpool finished second in the League that season behind Arsenal.

Houllier's time was up as manager at the end of the 2003/04 season when he was replaced by Rafael Benítez, who joined the club after a successful period as manager of Valencia in La Liga. Even though Liverpool's first league campaign under Rafa Benitez was disappointing when they finished fifth, the season's highlight was the incredible Champions League success at the Ataturk Stadium, Istanbul. Liverpool won the 2004–05 UEFA Champions League in sensational style, beating A.C. Milan 3–2 in a penalty shootout after the match ended with a score of 3–3. This after Liverpool were 3-0 down at half-time.

The following season, Liverpool finished third in the Premier League and won the 2006 FA Cup Final, beating West Ham United in a penalty shootout after the match finished on 3–3. This final has been renamed by many as the "Gerrard Final" after Steven Gerrards fabulous display and spectacular 35-yard equaliser in injury time.

A truly terrible spell in the club's history was only around the corner when two American businessmen, George Gillett and Tom Hicks, became the owners of the club during the 2006–07 season, in a deal which valued the club and its outstanding debts at about £218.9 million. The club reached the 2007 UEFA Champions League Final, again against AC Milan, as it had in 2005, but this time Liverpool lost 2–1. At the end of the 2008–09 season Liverpool reached 86 points, its highest Premier League points total, but still finished as runners up to Manchester United.

Liverpool's 2009–10 season was poor and they finished seventh in the Premier League and, as a result, failed to qualify for the Champions League. Rafa Benítez subsequently left by mutual consent and was replaced by Fulham manager Roy Hodgson. The situation with the existing American owners, Hicks and Gillet, was getting worse and the club were heavily involved in much in-house fighting and at the start of the 2010–11 season Liverpool were allegedly on the verge of bankruptcy. The club's creditors asked the High Court to allow the sale of the club, overruling the wishes of Hicks and Gillett. John W. Henry, owner of the Boston Red Sox and of New England Sports Ventures, bid successfully for the club and took ownership in October 2010. A string of poor results in the first half of the season led to Hodgson's tenure being a very short-lived affair and he also left the club by mutual consent and former manager, and huge fan's favourite, Kenny Dalglish took over.

In Dalglish's first full season, Liverpool won their first trophy for six years when they won the League Cup (Carling Cup) for a record eighth time when they defeated Cardiff in a dramatic penalty shoot-out at Wembley in February 2012.